Data requests

How to request data/analyses

Guillaume set up trac, a system for tracking requests for data and analyses. Please use this system for data requests from now on.

You can access this program at this address : http://edhar.genomecenter.ucdavis.edu/trac/ User name : iseem password : daffodil

It is currently set up with a common username for everyone due to security concerns. There are a couple functionalities that may not apply to us so feel free to overlook those.

The two main options for everyone is : View Tickets and New Ticket (after you log in). The one thing I want to point your attention towards is the "Assign to" text box for creating tickets. Please write the name of the person opening the ticket in that field so I can tell who is opening what ticket. It'll be a lot easier for me to keep track of things.

Request List from Dec 09 Meeting

• Josh
  • OTUs - from rRNA - from ocean PCR and metagenomic data
  • OPFs from metagenomic data
• James
  • OTUs filtered by narrower taxonomic range (e.g. families)
  • OTUs from both metagenomic and additional ocean PCR data
• Sam
  • Protein families
    • alignments, trees from metagenomic data for those families
  • Simulations
    • Generating and analyzing trees from simulated data
• Tom
  • All vs. all clustering of protein sequences from whole genome data
    • Build the families
• Dongying
  • Merge families from different phyla
    • MySQL database of relationships between taxonomy and sequences (map JGI <-> MicrobeDB?)
  • Install HMMER3 in centralized location
    • Get consensus sequences for HMM profiles to group HMMs/families into clusters
• Morgan
  • All vs. all BLASTs
  • Access to many metagenomic data sets with metadata (grab from CAMERA)?
• Steve
  • Alignments of metagenomic reads to more gene families (using AMPHORA?)
    • For GOS data set
    • Additional marker gene families from Dongying
    • Additional markers for different taxonomic groups (archaea, Actinos, etc.)